Install bokeh

  1. Install nodejs
    conda install -c conda-forge nodejs
  2. install jupyter lab
    conda install -c conda-forge jupyterlab
  3. install jupyter lab:
    jupyter labextension install
    jupyter labextension list
  4. install bokeh plugin for jupyter
    jupyter labextension install jupyterlab_bokeh

the useful plugins for new linux installation

  1. install virtualenvironment:
  2. Install open terminal here:
    sudo apt-get install nautilus-open-terminal
    nautilus -q
  3. install notebook extenstion
    pip install jupyter_contrib_nbextensions
    jupyter contrib nbextension install –user

Make string to a command in python


Use GO in Jupyter


Jupyter Magic Memory

  1. %: line magic, %%cell magic
  2. Repeat Command:
  3. Write cell content into a file:
  4. To autoreload your pyfile:
    %load_ext autoreload
    %autoreload 2
    from yourfile import yourFunction
  5. Use R in jupyter
    %load_ext rpy2.ipythonR magic in cell
    %%Rcode in line

    Move variable between R and python
    %Rpush, %Rpull
    R magic tutorial:
    R magic:
    Problem in rmagic:

  6. %store
    store variable between different ipython notebook

R important things

R has no block comment, but you can still do the following things:

  • In RStudio: Ctrl+Shift+C
  • if(false){xxx} block


python to R

df.tail() -> tail(df)

dropna(df) ->na.omit(df) / df[complete.cases(df),]

df.describe() -> summary(df), library(psych): describe(df)

df.shape -> dim(df)


Two ways to update docs in cursor objects with pymongo

I have a collection with:

name    weight    amount
apple     2               3
banana  2               5
pear       2               5

I want add a column about the total price, which is equal to weight * amount

name    weight    amount    total
apple     2               3              6
banana  2               5             10
pear       2               5            10

myFile = [
{"name":"apple", "weight":2, "amount":3}, 
{"name":"banana", "weight":2, "amount":5}, 
{"name":"pear", "weight":2, "amount":5}


Method 1: collection.find() + update_one()

fruits = testDB.db.testCollection.find({}, modifiers={"$snapshot": True})

for fruit in fruits:
    total = fruit['weight'] * fruit['amount']
    testDB.db.testCollection.update_one({"_id":fruit['_id']}, {'$set': {'total': total}})

# check the result:


Method 2: collection.aggregate() with $project, $multiply and $out

testDB.db.testCollection.aggregate([{'$project': {
        'total': {"$multiply": ["$weight",'$amount']}
      }}, {
# check the result

How to reference python variable in jupyter notebook markdown cell

  1. Install Jupyter notebook extension plugin:
    1. conda install -c conda-forge jupyter_contrib_nbextensions
    2. jupyter contrib nbextension install --user
  2. Go to Jupyter notebook
    1. click Nbextensions
    2. enable Python Markdown
  3. use {{python variable}} in markdown cell. ๐Ÿ™‚

pycharm for django and sass

For django:

professional version.

  1. create a new django project: just create a new one
  2. import a django project:
    1. import the project
    2. activate django support

For Sass:

  1. make sure, the sass support is activate: File -> Setting -> Plugin
  2. install node.js: File -> Setting -> Plugin -> install jetbrain plugin
  3. install ruby: during the installation, don’t forget check the option “set path to default”
  4. open teminal to install sass: “gem install sass”
  5. create a file watcher: File -> setting ->tools -> file watcher -> add -> sass
  6. transpiling the code

Cassandra, Python, R, Node.js

It is quite nice, that Cassandra has driver for Python, R and Node.js.

If you want to build a website with Cassandra DB which has also heavily scientific programming, I would suggest the following combination:

  1. Python Flask  or Django + Cassandra
  2. Python(ZeroMQ, zerorpc) + R(opencpu) + Nodejs + Cassandra

The first solution is easiest, but the second solution is more elegant since you can separate the Python, Cassandra, NodeJS in different server. Thus the advantages of Node.JS will be kept. Of course, you can also use the childprocess from nodejs to call the Python and R.